best suitable aligner for RNA-seq mapping

yueli · 04-19-2018, 07:37 AM

Hello,

Human RNA-seq dataset was generated from Illumina HiSeq 3000 with 2X100 cycles run.

The first step is making alignment of the reads to the human genome. These are many aligner, such as: Bowtie, GASSST, PASS, SOAP, BOAT. Each aligners has different performs in different kinds of data.

Which is the best suitable aligner for RNA-seq data?

Thank you in advance for great help!

Sincerely,

Yue

GenoMax · 04-19-2018, 07:47 AM

There is no "best" aligner in a practical sense. Most aligners will give you reasonable alignments that you should be able to use for expression analysis.

You want to make sure the aligner you use is "splice-aware" since you have human data. BBMap, STAR, HISAT2 are examples of such aligners.

yueli · 04-19-2018, 08:16 AM

Thanks for GenoMax response!

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04-19-2018, 07:47 AM	#2
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 6,994	There is no "best" aligner in a practical sense. Most aligners will give you reasonable alignments that you should be able to use for expression analysis. You want to make sure the aligner you use is "splice-aware" since you have human data. BBMap, STAR, HISAT2 are examples of such aligners.

04-19-2018, 08:16 AM	#3
yueli Member Location: china Join Date: May 2013 Posts: 71	Thanks for GenoMax response!